Assassin's Creed: Juno's End
by MercilessSun
Summary: After III, Desmond is in the Animus Matrix, where he goes through another ancestor's life to find a way to bring himself back to life, and defeat Juno.
1. Prologue

**Hello everyone and welcome to a new fanfiction. I know that I havent done much, but that's because I haven't been paying much attention to anime, and that means that I am abandoning Bleach Aizen's Revenge. Sorry. But here is my sequel to a great game known as Assassin's Creed 3. I have been watching the first 3 games, and played the other 2: Revelations and 3. But this has a new ancestor, and possibly...Lucy! Enjoy**

* * *

The way the world ends is not what you think. My name is Desmond Miles. I am from a long line of Assassins, warriors who fought against the Knights Templar. A Templar company known as Abstergo kidnapped me and brought me to Rome, where I was put in a machine named the Animus, where I viewed the memories of my ancestors.

I saw the life of Altair Ibn La'ahad, an 11th century Syrian Assassin whose master, Al Mualim, sent him to get an artifact from Solomon's Temple and failed. Al Mualim turned against the Order for complete control from the artifact known as the Apple of Eden. After Altair defeated him, he found a map of the other Pieces of Eden, which was Abstergo's goal. After I found it, through something known as the Bleeding Effect, I gained Eagle Vision and saw blood-written messages from the last Animus experiment, Subject 16.

The next day, Abstergo's lead scientist, Warren Vidic, almost killed me, but his assistant Lucy Stillman saved me and later on, freed me from Abstergo. I was taken to an Assassin hideout, where the Animus team there, Rebecca Crane and Shaun Hastings, took me into the Animus again for training to become an Assassin by seeing another ancestor, Ezio Auditore da Firenze, a 15th century Italian Assassin whose brothers and father were executed and fled with his mother and sister to his uncle Mario. He became an Assassin and removed Templar influence from Venice, Florence and Tuscany. Through the Codex pages hidden throughout Italy, he realized his destiny, to go into a temple in Rome and be given a message to pass onto me, to warn me that the Sun would cook the Earth in Dec. 21, 2012. After the training, Vidic found us. So we left to the old home of Ezio, the Villa Auditore.

Inside a hidden area there known as the Sanctuary, I saw Ezio end the reign of the Borgia family, a Templar family who stole the Apple of Eden from Ezio and also its most important member was the Pope. After he stopped them, he hid the Apple under the Coliseum in Rome. Lucy and I found it, but a woman from the First Civilization, Juno, controlled me and made me kill Lucy. I was horrified and put into a coma.

My dad plugged me into the Animus, where I met Subject 16. In there, I completed Altair's life, when he became the Mentor in Masyaf and hid his Apple in a hidden library and a secret location to the Grand Temple, and gave 5 keys to Marco Polo's father, Niccolo Polo. I also completed Ezio's life in Constantinople, where he got the Keys, ended the reign of the Byzantine Templars, met his future wife, Sofia Sartor, secured the Sultan's next heir, and gave me the location to the Grand Temple. I also looked at memories of my own life, when I was born, training to become an Assassin, left the life I was born into, and captured by Abstergo, but I also realized that no matter what, I am an Assassin. I woke up and led the team, including my dad, William Miles, to the Grand Temple in New York.

To unlock the door, I had to examine th lives of Haytham Kenway, an 18th century English Templar who made the Templar influence in Colonial America, and his Native American son, Ratonhnhaké:ton, or Connor, who killed the Templar leaders and helped General Washington free the Colonies by becoming an Assassin under Achilles Davenport's wing and buriesd the Grand Temple key in the Daenport homestead. Also, I explored the Grand Temple while being told by Juno what the First Civilization tried to do to avoid the first disaster. I got the key, unlocked the door and was given a choice by Minerva and Juno; (1) to help the wworld live and let Juno take the world, or (2) let the Sun release and have me become a Jesus-like figure and resume the old conflict. I chose Juno, but she killed me.

* * *

Jan. 5, 2013-Desmond woke up in a computer-like place. "Hello?"

He heard a familiar man's voice. "Quiet. Juno will hear you."

"Jupiter? Where am I?"

"This is the Animus Matrix, where the DNA database is. You are here to go through another ancestor's memories to find a way to defeat Juno."

"Alright. Get me in."

"I shall." He turned away and said, "Activate ancestor portal 7.2."

A digital voice said, "Portal to ancestor acitvated."

Jupiter said, "Good luck."

* * *

**There you go. Desmond is on his way to defat Juno. Stay tuned for...DNA Sequence 1-Greek Tales Born.**


	2. DNA Seqeunce 1-Greek Tales Made

**Hello everyone, and welcome back to Assassin's Creed: Juno's End. I hoped you enjoyed the first chapter. I hope you enjoy the locations and time. I guess I should explain about Desmond...Because of Desmond being in the Animus for too long, his Soul has been tied directly to it, so when he died, his soul was guided by Jupiter to the Animus Matrix.**

* * *

Desmond entered the Portal and was in Olympia, Greece in 795 B.C. He saw a boy being born. He wasn't surprised at all because it's not the first time he saw it. The child's father asked for a name and the mother said, "Isalus."

* * *

785 B.C. Isalus, now 10 years old, had short black hair, and was climbing a tree. His mother calling for him. He jumped onto his house and let go right in front of her. She jumped and asked, "How did you do that?"

"I just climbed the tree and onto the house, then I dropped."

"Well, please be careful. Now your father has something for you."

"Alright mother." He walked into his stone home and went to his father in the basement. "You wanted to see me?

His father had short black hair and a goatee."Yes. I believe I should explain that you are different than most people you age. You have a gift, a gift so amazing that anyone would love to have."

"Is that why I am able to see different things and climb better than most people?"

"Yes my family has had these abilities ever since the beginning of man. I wish to pass on some equipment. He gave Isalus leather bracers, and wooden sword, and gloves. "I will give you a real sword when you are responsible to wield one."

"Thank you, father."

* * *

776 B.C.-Isalus had moved away from his parents, obtained his father's sword, and lived with his girlfriend Metis. He had gotten a job as a scroll library bodyguard. He had gotten a day off, and was at the market.

He heard a 50 year old man say, "Read about the new era. Read the Theogony."

Isalus walked up to the old man and said, "What is this?"

"Finally someone who cares. This is the Theogony, stories I wrote about deities that 'created' us."

"Sounds amazing."

"Then come with me."

Isalus entered the home of the old man and saw a mess of papers showing gods and designs for objects.

The old man said, "I meant to say this earlier, my name is Hesiod."

"Isalus. So can I read this?"

"Of course."

Isalus read the story of a formless entity named Chaos that created deities that made the world, then of 6 gods that killed Titans to rule Earth. The gods mated to make 8 other gods to make the Olympian Gods on top of Mount Olympus, leaving 2 of the original gods behind.

Isalus said, "This is amazing."

"I'm glad you think so. No one really cares. "The day will come. I really like the goddess Athena."

"She is good. I would like you to keep that."

"Thanks again. Good-bye Hesiod."

He left and told Metis of what happened. Eventually all of Greece was reading the Theogony. Isalus then started seeing violence because of a cult named the Followers of Zeus. So he made a grey cloak with an upsides down v with some points on the bottom on the back of it. His friend 'Hephaestus' made him 2 daggers that can be attached to his bracers. He then had multiple friends that also thought that true order should be established. So they made a base in a cave in Mount Olympus.

**End of Sequence.**

* * *

Desmond was then in a dark room and yelled, "Jupiter!"

"Silence." He waited a few seconds and heard a woman say, "What's happening?" It was Juno.

Jupiter said, "Nothing."

Juno left , then Desmond got out of the dark room. "Where was I?"

"The Chaos Chamber. You must be quiet there." Alright. This has been amazing."

"I'm glad you like it, but must focus."

"Right."

"Now rest. I'll put you back in the Chaos Chamber."

"Alright."

* * *

A few hours ago, Empire State Building.

Rebecca was checking her previous entries from the Animus and saw some weird readings. "Hey Shaun. Check this out."

"What now?"

"I found some similar signatures in a new ancestor."

"Who?"

"It doesn't say. But I found what looks like Desmond's DNA there."

William heard that, and said, "What?"

"You heard right. Apparently, he may not be dead. It says the ancestor is from 8th century BC Greece."

Will said, "When I was training, I heard rumors of the first Assassin HQ in Olympia, Greece. Keep looking."

* * *

**There you go. The new Isalus has read what is called the Theogony or, Clash of the Titans. I have watched a Templar documentary and saw that they were founded around the 11th century, so I wondered, who would come before the army of God. So now you have the Followers of Zeus, who was considered God. Stay tuned for DNA Sequence 2-Olympian Clans Created.**


	3. DNA Sequence 2-Olympian Clans Made

**Hello everyone and welcome back to Assassin's Creed: Juno' End. I know I haven't been on for a while, but I was 'busy' playing Borderlands 2. So now, before we start this, I want to clear some things: 1) Isalus is the first ancestor to form the Assassins, because if you remember on the first game, Al Mualim said that for a couple thousand years, there once was an organization; 2) I was thinking if there should be an Apple of Eden, and yes there will be one, but it won't be the only Piece of Eden. Also, I was trying to make this somewhat historically accurate, but Brotherhood isn't either. So without further distraction, I bring you DNA Sequence 2-Olympian Clans Made.**

* * *

Desmond woke up in the Chaos Chamber. It disintegrated before him and Jupiter said, "Ready?"

"Yes."

Jupiter activated the portal and Desmond went in.

* * *

775 B.C. Mount Olympus. Isalus was with several architects as they were making chambers for his new warriors who named themselves the Athenian Assassins. Above the cave entrance was a carving that said, 'Tipota den eínai alithinó. Ta pánta epitrépontai.'

Isalus said, "Alright. Be sure to make some vents so the Hephaestus Blacksmiths don't die from the smoke."

His friend and apprentice, Nickolaes said, "The farmers have set up the reserves, we have a brothel, the thieves have settled in, and the mercenaries."

"Excellent. The Olympian Clans are coming together very well. How are the Followers of Zeus?"

They have heralds preaching to the people. Also soldiers are harassing the citizens for the heralds. I suggest we do something about it."

"Fine. I'll get things ready. You get our people training. While I'm gone, you watch the progress of the headquarters."

"Yes, sir."

Isalus went to the Hermes thieves and told them to steal a map to all heralds.

Then he went to the Aphrodite courtesans to distract the guards when they got there. He then went to th market to think of what to do.

Something caught his eye. He found someone selling poison. He bought a vial and it showed it to the thieves and had an idea to cover the tips of his hidden daggers in it.

He came back to Mount Olympus and Nickolaes was waiting for him. "We found something. Please follow me."

They walked down inside the mountain and found walls with blue outlines on it. Then there was a big chamber with an orange olive branch and a green gauntlet.

Isalus walked to them and touched the olive branch, then he was in a black and gold room with a grey-haired man.

"Greetings, young Assassin. My name is Jupiter. You have found 2 Pieces of Eden. I know you may not understand, but you must protect these items."

He turned away and said, "Desmond, when you are done here, contact your friends and tell them of the Uniter of Eden, the olive branch that can separate or reunite a soul with its body, and the Gauntlet of Eden, it will strip Juno of her powers.

Jupiter disappeared, and Isalus had many surrounding the Pieces of Eden, Jupiter, and 'Desmond.'

Before he left, he had 2 Assassins guard the Pieces of Eden.

When he came home, Metis said that there was a message for him. It was from a man named Golius.

It read, "There is only one Olympian that should exist. Meet me near Zeus' throne in 3 days."

He went back to the Athenian Assassins and told Nickolaes of Golius' message. So they had Isalus stay in Mount Olympus until their meeting, while they had some Assassin recruits secretly kill the heralds. **End of Sequence.**

* * *

Desmond the appeared in the Chaos Chamber. A minute later, he was back in the Animus Matrix.

He said, "You could have told me about the Pieces of Eden after the memory, not during when it could confuse Isalus."

"Sorry, but that is your goal. Now give them the message."

"Fine."

A window appeared, and Desmond spoke some words. When he was done, he went back into the Chaos Chamber.

* * *

Rebecca was looking into the unknown DNA file when a video popped up. It was Desmond. He said, "Hey guys. I don't have much time to explain. So here it is, my soul is alive, Jupiter is helping me find the answer to bringing me back to live and defeating Juno. So I want you to go to Mount Olympus, and try to find them. Take care everyone."

After the message was said, it deleted itself.

William said, "What are we waiting for? Let's bring my son back."

* * *

**There you go. Desmond found the answer to defeating Juno, but the story of Isalus is not over. Rebecca, Shaun and William found out that Desmond is alive, and are going to find the 2 new Pieces of Eden, the Uniter and Gauntlet. Also that carving in the cave entrance says 'Nothing is true. Everything is permitted,' in Greek. Stay tuned for DNA Sequence 3-Balance Restored.**


	4. DNA Sequence 3-Balance Restored

**Hey, everyone and welcome to a very interesting addition to Assassin's Creed: Juno's End. This going to be the end of Isalus, but not the end of the story. Enjoy.**

* * *

Mount Olympus, Present Day. Rebecca, Shaun and William went inside the cave and found an empty First Civilization room, but with no Pieces of Eden.

Shaun said, "Just as I suspected, he was wrong."

Will said, "He's not wrong, he's probably got the wrong location."

Rebecca said, "I'll send Desmond a message to tell him the news." She traced the signal from his message and sent one to him. "Let's hope he can hurry."

* * *

Desmond woke up and was greeted by Jupiter.

"You received a message from your friends. Run video file R3b3cca 1."

There was a video message that said, "Hey Desmond. It's great to hear from you. Look, we found the cave, but we couldn't find anything. Please let us know where they are. And please hurry, because Juno is bringing hell to everyone."

Desmond said, "Let's find where Isalus put them."

Jupiter activated the portal and Desmond entered.

* * *

775 B.C. Mount Olympus. Isalus was writing on some paper about the secrets of the Assassins, and also made a white outfit with a hood and some sashes for his weapons.

After 3 days, he went to Zeus' throne and found Golius with an orange orb. "At last, the Gods will allow me to settle this once and for all!" He held the orb in the air, and Isalus was in a great amount of pain as he slowly brought his hidden dagger to his neck.

However, Isalus focused very hard , broke free, threw the dagger into Golius' hand, and he dropped the orb.

Golius said, "The Apple of Eden is mine!"

Isalus pulled the Uniter of Eden out from his robes, release Golius' soul from his body and said, "Not today."

He picked up the Apple, and appeared in that black-and-gold room, but with a brown-haired woman. "My name is Minerva. I thank you for defeating Golius, for he was not worthy. However, you are, and may carry this without insanity. Now spread your knowledge to the east."

Minerva disappeared and Isalus returned to the throne. He picked up his dagger and returned to the Athenian Assassins. He told Nickolaes to copy the assassination techniques, then took the journal, Pieces of Eden, took his belonging, and brought Metis away from Greece.

* * *

762 B.C. Masyaf, Syria-He made an Assassin Den, had a 7 year old son named Aetós, and a 3 year old daughter named Spourgítis. He hid the Pieces of Eden in the mountain.

* * *

July 25 751 B.C. Isalus was training Assassins, one of them being Aetós, now 16. It was their last day as novices.

* * *

Next day-They had been initiated as real Assassins. Then Isalus got a message that the Followers of Zeus declared war against the Athenian Assassins and that the only surviving Assassin was Nickolaes, and that he was coming to Masyaf.

* * *

749 B.C. Jerusalem-Nickolaes moved in there, made several Dens, and had a son named Geráki, who would eventually be the ancestor of Abbas.

* * *

738 B.C. Masyaf-Isalus, with his son and his child, Alta, were watching for Followers. Aetós never told Alta of the Assassins, so he could be free. Meanwhile, his sister fled to Florence, Italy with a man, and eventually become ancestors to Domenico Auditore.

* * *

720 B.C. Masyaf-Isalus was on his deathbed, telling Aetós and Alta to protect the Pieces of Eden. Before Isalus was buried, Aetós took Isalus' robes and places them in a chest with the Pieces of Eden. Alta would be oblivious of the Assassins until his son found Isalus's journal in 682 B.C. However he never wanted to become an Assassin.

**End of Sequence.**

* * *

Desmond was in the Chaos Camber once again, but Juno never appeared.

He was back in the Animus Matrix with Jupiter. Desmond asked, "Is that the end of the memories?"

"No. Tomorrow, you shall complete 1 last sequence to find the location in Masyaf. But you can tell your friends that they are in Masyaf."

The window appeared and Desmond spoke the message the went to bed in the Chaos Chamber.

* * *

The Animus team was outside of Mount Olympus when Rebecca got the message.

"Hey. Sorry about leading you the wrong way. Turns out I wasn't done with the memories. Now the Pieces of Eden are at Masyaf. I'm not entirely sure where, but they are at Masyaf. Goodbye, and I shall see you guys soon."

Rebecca said, "Finally. Alright. Let's pack up and go to Masyaf."

* * *

**And that's the end of Isalus, but as you see, it's not finished yet. His descendent, which you will soon recognize, will show Desmond the true location. Stay tuned for Assassin's Creed: Juno's End...The Legendary Mentor. And to be in the spirit of Assassin's Creed, I had Isalus' kids, and Nickolaes' son be named after birds; the son 'Eagle', the daughter 'Sparrow', and Nickolaes' son 'Hawk.' Review or PM me and tell me how it is. This is MercilessSun, signing off.**


	5. DNA Sequence 4-The Legendary Mentor

**Hey, guys. Welcome back to Assassin's Creed: Juno's End. I know it's been a while, but I was 'busy' playing AC 1, 2, and 3. So here is the Final DNA Sequence.**

* * *

Desmond woke up and appeared in the Animus Matrix with Jupiter.

"You have another message. Run video file R3b3cca 2."

A video popped up and Rebecca said, "Hey, Desmond. Thanks for the correction. We'll be right there. See you soon." The video disappeared.

Desmond said, "Let's finish this. Get me in."

Jupiter opened the portal and Desmond went in.

* * *

1191 A.D. Masyaf. Altair went into his family home, before the going to Solomon's Temple. He uncovered a chest with an olive branch and a gauntlet. Also there was a scroll. He unrolled it, but it was in Ancient Greek.

He rode to a translator in Acre and it said, "The contents inside must be protected until 'Desmond' finds it."

Back in Masyaf, Altair hid the chest back where it was.

* * *

1257 A.D. Masyaf-Altair was now the Mentor and was writing extra pages to his Codex about the Pieces of Eden and 'Desmond', when Niccolo and Maffeo Polo were about to leave to Constantinople. He told his son to take the Pieces of Eden to the Library under the fortress.

After Altair escorted the Polo brothers, he went inside the Library, put the Apple of Eden in the hiding place, put the extra Codex pages on a shelf next to the Pieces of Eden, got the Memory Seal, and died.

* * *

1512 A.D. Masyaf-Ezio Auditore was in Altair's Library, viewed the last Memory Seal, said his message to Desmond, then saw an olive branch and a gauntlet, along with 2 Codex pages.

Using some translation techniques he learned for Leonardo da Vinci, the 1st page said, "Before I die, I must fulfill my duty as guardian of 2 others Pieces of Eden, as it was my family's duty. I sent my son to put them in the library, while I protect the Polo brothers.

I must protect the Pieces until someone named 'Desmond' finds them."

The 2nd page said, "I once used the Pieces of Eden and they are powerful. The olive branch, or the Uniter, can separate or rejoin a person's soul with its body. The gauntlet is something that is best not explained.

I hope Desmond knows whether his intentions are good."

Ezio put the pages back and left. **End of Sequence.**

* * *

That is all for this chapter. I know it was short, but I hope you like what comes up next...Stay tuned for the Finale-Juno's End.


	6. Epilogue-Juno's End

Welcome to the Finale of Assassin's Creed: Juno's End. I thank you for reading this, and I really would like to thank my fans from Greece, because I want you to correct me on my bad history. I know that Ubisoft does a lot of work on that, while I go quarter-assed. So here is the end.

* * *

Back in the Chaos Chamber, Juno was outside for a few seconds, then broke into it. She angrily said, "I knew you couldn't leave well enough alone. You will not deny me my power!"

Jupiter then appeared, took Desmond, and vanished.

They were inside the library with Desmond's body. Jupiter said,"Get your friends over here."

* * *

In Masyaf, Rebecca was looking at Desmond's previous memories when her computer started changing into Desmond's face.

He said, "Quick, get into Altair's Library! Jupiter and I will be there!"

Rebecca said, "Alright, let's move."

William, Shaun and Rebecca went inside the Library, saw 2 Pieces of Eden and Desmond's body.

They saw Desmond's soul, along with Jupiter. Desmond said, "Please put the olive branch on my body."

Rebecca put the Uniter of Eden on his body and Desmond came back to life. He saw his dad walk towards him, and he hugged William.

Desmond let go and said, "It's not over yet."

He grabbed the Gauntlet and went outside. He walked through the fortress and into the garden. There, he was confronted by Juno.

She said, "My plans will not be disrupted, and your 2nd death will prove that."

Desmond put on the Gauntlet, and armor formed over his clothes. In a few seconds, he had platinum armor with eagle feather scales on the chest plate and a flexible metal Assassin's hood.

With a techno-voice, Desmond said, "As the Genesis Knight, I will kill the disruptor of peace. You, Juno, shall be wiped from this earth!

The Sword of Eden appeared in his hand, and chains wrapped around Juno's limbs. With one strike, Juno was killed.

Rebecca said, "Finally, it's over."

The armor disappeared, and Desmond said, "Not yet. We gotta get to Rome."

* * *

They got on a plane to Rome, drove to a graveyard, and saw a tombstone that said, "Lucy Stillman (1988-Oct. 10, 2012)."

He dug up her body and brought her back to life. Lucy gasped and coughed until she saw Desmond. "Where am I?"

"Rome. Look, back in the Coliseum, I was controlled by one of the Ancients, and kiled, you, but I ended this, and brought you back to life."

She hugged Desmond while crying a little and said, "Thank you."

Lucy saw William coming, and she slapped him. "That's for keeping me in Abstergo for a decade, you asshole!"

Desmond grabbed onto her shoulder, and she kissed him. "Thank you. Look, while I was in Abstergo, I switched to the Templ-"

"I know. When I was being controlled, the Ancient told me."

"But I'll be an Assassin again."

"Thank you."

* * *

10 years later-Desmond moved out of Manhattan, and back to 'The Farm.' He and Lucy brought out the secrets of Abstergo, and shut them down. They had a daughter named Claudia, and she was training to become an Assassin.

* * *

I thank you for reading this. Please review and read some of my other fanfictions. This is MercilessSun, and I thank you for reading Assassin's Creed: Juno's End.


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